Fig. 2. Two coordinated waves of ZGA during ascidian embryogenesis.

a Illustration of reads mapped to C. robusta and C. savignyi genomes at different developmental stages. Horizontal and vertical axes represent genome position and log₂-transformed read number in each window, respectively. The bright red and bright blue indicated C. robusta and C. savignyi, while the light red and light blue indicated the forward and reverse cross samples, respectively. b read count ratios of paternal genes to all genes at different developmental stages. The red arrows indicated the two waves during ZGA. c Ratio of number of de-novo transcribed paternal genes to number of all paternal genes at different developmental stages. The red arrows indicated the minor and major ZGA which corresponded with the initiation of zygotic gene expression and housekeeping gene reactivation, respectively. d Heat map of H3K27ac CUT&Tag signals across activated genes and housekeeping genes in reverse cross hybrid embryos. Each line shows the normalized signals for a gene from -2k bp above TSS to +2k bp below TES. The number in parentheses indicated the de-novo transcribed gene number in each stage. e Heatmap of paternal gene expression in different modules in forward cross embryos. Module 1 included minor wave genes, the expression of which increased from the 16- to 32-cell stage, whereas modules 2 and 3 included major wave genes, the expression of which increased from the 64- to 112-cell stage. f Heatmap of paternal gene expression in different modules in reverse cross embryos. The description of the modules given in (e) also applies here. Source data are provided as a Source Data file.